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Package Hierarchies:
de.jstacs
,
de.jstacs.algorithms
,
de.jstacs.algorithms.graphs
,
de.jstacs.algorithms.graphs.tensor
,
de.jstacs.algorithms.optimization
,
de.jstacs.algorithms.optimization.termination
,
de.jstacs.classifier
,
de.jstacs.classifier.assessment
,
de.jstacs.classifier.modelBased
,
de.jstacs.classifier.scoringFunctionBased
,
de.jstacs.classifier.scoringFunctionBased.gendismix
,
de.jstacs.classifier.scoringFunctionBased.logPrior
,
de.jstacs.classifier.scoringFunctionBased.msp
,
de.jstacs.classifier.utils
,
de.jstacs.data
,
de.jstacs.data.alphabets
,
de.jstacs.data.bioJava
,
de.jstacs.data.sequences
,
de.jstacs.data.sequences.annotation
,
de.jstacs.io
,
de.jstacs.models
,
de.jstacs.models.discrete
,
de.jstacs.models.discrete.homogeneous
,
de.jstacs.models.discrete.homogeneous.parameters
,
de.jstacs.models.discrete.inhomogeneous
,
de.jstacs.models.discrete.inhomogeneous.parameters
,
de.jstacs.models.discrete.inhomogeneous.shared
,
de.jstacs.models.mixture
,
de.jstacs.models.mixture.gibbssampling
,
de.jstacs.models.mixture.motif
,
de.jstacs.models.mixture.motif.positionprior
,
de.jstacs.models.utils
,
de.jstacs.motifDiscovery
,
de.jstacs.motifDiscovery.history
,
de.jstacs.parameters
,
de.jstacs.parameters.validation
,
de.jstacs.results
,
de.jstacs.scoringFunctions
,
de.jstacs.scoringFunctions.directedGraphicalModels
,
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures
,
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures
,
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures
,
de.jstacs.scoringFunctions.homogeneous
,
de.jstacs.scoringFunctions.mix
,
de.jstacs.scoringFunctions.mix.motifSearch
,
de.jstacs.utils
,
de.jstacs.utils.random
Class Hierarchy
java.lang.
Object
de.jstacs.algorithms.optimization.termination.
AbsoluteValueCondition
(implements de.jstacs.algorithms.optimization.termination.
TerminationCondition
)
de.jstacs.classifier.
AbstractClassifier
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.classifier.
AbstractScoreBasedClassifier
de.jstacs.classifier.
MappingClassifier
de.jstacs.classifier.modelBased.
ModelBasedClassifier
de.jstacs.models.discrete.inhomogeneous.shared.
SharedStructureClassifier
de.jstacs.classifier.scoringFunctionBased.
ScoreClassifier
de.jstacs.classifier.scoringFunctionBased.gendismix.
GenDisMixClassifier
de.jstacs.classifier.scoringFunctionBased.msp.
MSPClassifier
java.util.
AbstractCollection
<E> (implements java.util.
Collection
<E>)
java.util.
AbstractList
<E> (implements java.util.
List
<E>)
java.util.
ArrayList
<E> (implements java.lang.
Cloneable
, java.util.
List
<E>, java.util.
RandomAccess
, java.io.
Serializable
)
de.jstacs.parameters.
ParameterSet.ParameterList
de.jstacs.models.
AbstractModel
(implements java.lang.
Cloneable
, de.jstacs.models.
Model
, de.jstacs.
Storable
)
de.jstacs.models.mixture.
AbstractMixtureModel
de.jstacs.models.mixture.motif.
HiddenMotifMixture
(implements de.jstacs.motifDiscovery.
MotifDiscoverer
)
de.jstacs.models.mixture.motif.
SingleHiddenMotifMixture
de.jstacs.models.mixture.
MixtureModel
de.jstacs.models.discrete.inhomogeneous.shared.
SharedStructureMixture
de.jstacs.models.mixture.
StrandModel
de.jstacs.models.
CompositeModel
de.jstacs.models.discrete.
DiscreteGraphicalModel
(implements de.jstacs.
InstantiableFromParameterSet
)
de.jstacs.models.discrete.homogeneous.
HomogeneousModel
de.jstacs.models.discrete.homogeneous.
HomogeneousMM
de.jstacs.models.discrete.inhomogeneous.
InhomogeneousDGM
de.jstacs.models.discrete.inhomogeneous.
DAGModel
de.jstacs.models.discrete.inhomogeneous.
BayesianNetworkModel
de.jstacs.models.discrete.inhomogeneous.
FSDAGModel
de.jstacs.models.mixture.gibbssampling.
FSDAGModelForGibbsSampling
(implements de.jstacs.models.mixture.gibbssampling.
GibbsSamplingComponent
)
de.jstacs.models.
NormalizableScoringFunctionModel
de.jstacs.models.
UniformModel
de.jstacs.models.
VariableLengthWrapperModel
de.jstacs.scoringFunctions.
AbstractNormalizableScoringFunction
(implements de.jstacs.scoringFunctions.
NormalizableScoringFunction
)
de.jstacs.scoringFunctions.mix.
AbstractMixtureScoringFunction
de.jstacs.scoringFunctions.mix.motifSearch.
HiddenMotifsMixture
(implements de.jstacs.motifDiscovery.
MutableMotifDiscoverer
)
de.jstacs.scoringFunctions.mix.
MixtureScoringFunction
(implements de.jstacs.motifDiscovery.
MutableMotifDiscoverer
)
de.jstacs.scoringFunctions.mix.
VariableLengthMixtureScoringFunction
(implements de.jstacs.scoringFunctions.
VariableLengthScoringFunction
)
de.jstacs.scoringFunctions.mix.
StrandScoringFunction
(implements de.jstacs.motifDiscovery.
Mutable
)
de.jstacs.scoringFunctions.
AbstractVariableLengthScoringFunction
(implements de.jstacs.scoringFunctions.
VariableLengthScoringFunction
)
de.jstacs.scoringFunctions.
CMMScoringFunction
de.jstacs.scoringFunctions.homogeneous.
HomogeneousScoringFunction
de.jstacs.scoringFunctions.homogeneous.
HMM0ScoringFunction
de.jstacs.scoringFunctions.homogeneous.
HMMScoringFunction
de.jstacs.scoringFunctions.homogeneous.
UniformHomogeneousScoringFunction
de.jstacs.scoringFunctions.directedGraphicalModels.
BayesianNetworkScoringFunction
(implements de.jstacs.
InstantiableFromParameterSet
)
de.jstacs.scoringFunctions.directedGraphicalModels.
MutableMarkovModelScoringFunction
(implements de.jstacs.motifDiscovery.
Mutable
)
de.jstacs.scoringFunctions.
IndependentProductScoringFunction
(implements de.jstacs.motifDiscovery.
MutableMotifDiscoverer
)
de.jstacs.scoringFunctions.
MRFScoringFunction
de.jstacs.scoringFunctions.
NormalizedScoringFunction
(implements de.jstacs.motifDiscovery.
Mutable
)
de.jstacs.scoringFunctions.mix.motifSearch.
PositionScoringFunction
de.jstacs.scoringFunctions.mix.motifSearch.
DurationScoringFunction
de.jstacs.scoringFunctions.mix.motifSearch.
MixtureDuration
de.jstacs.scoringFunctions.mix.motifSearch.
SkewNormalLikeScoringFunction
de.jstacs.scoringFunctions.mix.motifSearch.
UniformDurationScoringFunction
de.jstacs.scoringFunctions.
UniformScoringFunction
de.jstacs.io.
AbstractStringExtractor
(implements java.util.
Enumeration
<E>)
de.jstacs.io.
InfixStringExtractor
de.jstacs.io.
LimitedStringExtractor
de.jstacs.io.
SimpleStringExtractor
de.jstacs.io.
SparseStringExtractor
de.jstacs.io.
StringExtractor
de.jstacs.algorithms.
Alignment
de.jstacs.algorithms.
Alignment.SimpleCosts
(implements de.jstacs.algorithms.
Alignment.Costs
)
de.jstacs.algorithms.
Alignment.StringAlignment
de.jstacs.data.
Alphabet
(implements java.lang.
Comparable
<T>, de.jstacs.
InstantiableFromParameterSet
, de.jstacs.
Storable
)
de.jstacs.data.alphabets.
ContinuousAlphabet
de.jstacs.data.alphabets.
DiscreteAlphabet
de.jstacs.data.alphabets.
ComplementableDiscreteAlphabet
de.jstacs.data.alphabets.
DNAAlphabet
de.jstacs.data.
AlphabetContainer
(implements java.lang.
Comparable
<T>, de.jstacs.
InstantiableFromParameterSet
, de.jstacs.
Storable
)
de.jstacs.io.
ArrayHandler
de.jstacs.data.bioJava.
BioJavaAdapter
de.jstacs.models.mixture.gibbssampling.
BurnInTest
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.models.mixture.gibbssampling.
AbstractBurnInTest
de.jstacs.models.mixture.gibbssampling.
VarianceRatioBurnInTest
de.jstacs.models.mixture.gibbssampling.
SimpleBurnInTest
de.jstacs.motifDiscovery.history.
CappedHistory
(implements de.jstacs.motifDiscovery.history.
History
)
de.jstacs.scoringFunctions.mix.motifSearch.
CDFOfNormal
de.jstacs.algorithms.graphs.
Chu_Liu_Edmonds
de.jstacs.classifier.utils.
ClassificationVisualizer
de.jstacs.classifier.assessment.
ClassifierAssessment
de.jstacs.classifier.assessment.
KFoldCrossValidation
de.jstacs.classifier.assessment.
RepeatedHoldOutExperiment
de.jstacs.classifier.assessment.
RepeatedSubSamplingExperiment
de.jstacs.classifier.assessment.
Sampled_RepeatedHoldOutExperiment
de.jstacs.models.discrete.inhomogeneous.
CombinationIterator
de.jstacs.algorithms.optimization.termination.
CombinedCondition
(implements de.jstacs.algorithms.optimization.termination.
TerminationCondition
)
de.jstacs.utils.
ComparableElement
<E,C> (implements java.lang.
Comparable
<T>)
de.jstacs.classifier.
ConfusionMatrix
(implements de.jstacs.
Storable
)
de.jstacs.algorithms.optimization.
ConstantStartDistance
(implements de.jstacs.algorithms.optimization.
StartDistanceForecaster
)
de.jstacs.models.discrete.
Constraint
(implements de.jstacs.
Storable
)
de.jstacs.models.discrete.homogeneous.
HomogeneousModel.HomCondProb
de.jstacs.models.discrete.inhomogeneous.
InhConstraint
(implements java.lang.
Cloneable
)
de.jstacs.models.discrete.inhomogeneous.
InhCondProb
de.jstacs.models.discrete.inhomogeneous.
MEMConstraint
de.jstacs.models.discrete.
ConstraintManager
de.jstacs.parameters.validation.
ConstraintValidator
(implements de.jstacs.parameters.validation.
ParameterValidator
)
de.jstacs.algorithms.graphs.
DAG
de.jstacs.utils.
DefaultProgressUpdater
(implements de.jstacs.utils.
ProgressUpdater
)
de.jstacs.utils.
TimeLimitedProgressUpdater
de.jstacs.algorithms.optimization.
DifferentiableFunction
(implements de.jstacs.algorithms.optimization.
Function
)
de.jstacs.classifier.scoringFunctionBased.logPrior.
LogPrior
(implements de.jstacs.
Storable
)
de.jstacs.classifier.scoringFunctionBased.logPrior.
CompositeLogPrior
de.jstacs.classifier.scoringFunctionBased.logPrior.
DoesNothingLogPrior
de.jstacs.classifier.scoringFunctionBased.logPrior.
SeparateLogPrior
(implements java.lang.
Cloneable
)
de.jstacs.classifier.scoringFunctionBased.logPrior.
SeparateGaussianLogPrior
de.jstacs.classifier.scoringFunctionBased.logPrior.
SeparateLaplaceLogPrior
de.jstacs.classifier.scoringFunctionBased.logPrior.
SimpleGaussianSumLogPrior
de.jstacs.algorithms.optimization.
NegativeDifferentiableFunction
de.jstacs.algorithms.optimization.
NumericalDifferentiableFunction
de.jstacs.classifier.scoringFunctionBased.
OptimizableFunction
de.jstacs.classifier.scoringFunctionBased.
AbstractOptimizableFunction
de.jstacs.classifier.scoringFunctionBased.
AbstractMultiThreadedOptimizableFunction
de.jstacs.classifier.scoringFunctionBased.
SFBasedOptimizableFunction
de.jstacs.classifier.scoringFunctionBased.gendismix.
LogGenDisMixFunction
de.jstacs.models.utils.
DiscreteInhomogenousSampleEmitter
de.jstacs.data.
DiscreteSequenceEnumerator
(implements de.jstacs.data.
RecyclableSequenceEnumerator
)
de.jstacs.utils.
DoubleList
(implements de.jstacs.
Storable
)
de.jstacs.algorithms.graphs.
Edge
(implements java.lang.
Cloneable
, java.lang.
Comparable
<T>)
javax.swing.filechooser.
FileFilter
de.jstacs.io.
RegExFilenameFilter
(implements java.io.
FileFilter
, java.io.
FilenameFilter
)
de.jstacs.io.
FileManager
de.jstacs.parameters.
FileParameter.FileRepresentation
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.utils.
GUIProgressUpdater
(implements java.awt.event.
ActionListener
, de.jstacs.utils.
ProgressUpdater
)
de.jstacs.utils.
IntList
de.jstacs.algorithms.optimization.termination.
IterationCondition
(implements de.jstacs.algorithms.optimization.termination.
TerminationCondition
)
de.jstacs.motifDiscovery.
KMereStatistic
de.jstacs.algorithms.optimization.
LimitedMedianStartDistance
(implements de.jstacs.algorithms.optimization.
StartDistanceForecaster
)
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.
Measure
(implements java.lang.
Cloneable
, de.jstacs.
InstantiableFromParameterSet
, de.jstacs.
Storable
)
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.
BTExplainingAwayResidual
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.
BTMutualInformation
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.
InhomogeneousMarkov
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.
PMMExplainingAwayResidual
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.
PMMMutualInformation
de.jstacs.models.utils.
ModelTester
de.jstacs.motifDiscovery.
MotifDiscovererToolBox
de.jstacs.motifDiscovery.
MutableMotifDiscovererToolbox
de.jstacs.motifDiscovery.
MotifDiscoveryAssessment
de.jstacs.utils.random.
MRGParams
de.jstacs.utils.random.
DiMRGParams
de.jstacs.utils.random.
DirichletMRGParams
de.jstacs.utils.random.
FastDirichletMRGParams
de.jstacs.utils.random.
ErlangMRGParams
de.jstacs.algorithms.graphs.
MST
de.jstacs.utils.random.
MultivariateRandomGenerator
de.jstacs.utils.random.
DirichletMRG
de.jstacs.utils.random.
EqualParts
de.jstacs.utils.random.
ErlangMRG
de.jstacs.utils.random.
SoftOneOfN
de.jstacs.algorithms.optimization.
NegativeFunction
(implements de.jstacs.algorithms.optimization.
Function
)
de.jstacs.motifDiscovery.history.
NoRevertHistory
(implements de.jstacs.motifDiscovery.history.
History
)
de.jstacs.utils.
Normalisation
de.jstacs.utils.
NullProgressUpdater
(implements de.jstacs.utils.
ProgressUpdater
)
de.jstacs.data.sequences.annotation.
NullSequenceAnnotationParser
(implements de.jstacs.data.sequences.annotation.
SequenceAnnotationParser
)
de.jstacs.parameters.validation.
NumberValidator
<E> (implements de.jstacs.parameters.validation.
ParameterValidator
)
de.jstacs.algorithms.optimization.
OneDimensionalFunction
(implements de.jstacs.algorithms.optimization.
Function
)
de.jstacs.algorithms.optimization.
NegativeOneDimensionalFunction
de.jstacs.algorithms.optimization.
OneDimensionalSubFunction
de.jstacs.algorithms.optimization.
QuadraticFunction
de.jstacs.algorithms.optimization.
Optimizer
java.io.
OutputStream
(implements java.io.
Closeable
, java.io.
Flushable
)
de.jstacs.utils.
SafeOutputStream
de.jstacs.parameters.
Parameter
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.parameters.
CollectionParameter
(implements de.jstacs.parameters.
Rangeable
)
de.jstacs.parameters.
EnumParameter
de.jstacs.parameters.
MultiSelectionCollectionParameter
(implements de.jstacs.parameters.
RangeIterator
)
de.jstacs.classifier.
MeasureParameters
de.jstacs.parameters.
FileParameter
de.jstacs.parameters.
ParameterSetContainer
(implements de.jstacs.parameters.
Rangeable
, de.jstacs.parameters.
RangeIterator
)
de.jstacs.parameters.
RangeParameter
(implements de.jstacs.parameters.
RangeIterator
)
de.jstacs.parameters.
SimpleParameter
(implements de.jstacs.parameters.
Rangeable
)
de.jstacs.scoringFunctions.directedGraphicalModels.
Parameter
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.parameters.
ParameterSet
(implements java.lang.
Cloneable
, de.jstacs.parameters.
RangeIterator
, de.jstacs.
Storable
)
de.jstacs.classifier.assessment.
ClassifierAssessmentAssessParameterSet
de.jstacs.classifier.assessment.
KFoldCVAssessParameterSet
de.jstacs.classifier.assessment.
RepeatedHoldOutAssessParameterSet
de.jstacs.classifier.assessment.
RepeatedSubSamplingAssessParameterSet
de.jstacs.classifier.assessment.
Sampled_RepeatedHoldOutAssessParameterSet
de.jstacs.parameters.
ExpandableParameterSet
de.jstacs.data.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
de.jstacs.parameters.
ArrayParameterSet
de.jstacs.data.
AlphabetContainerParameterSet.AlphabetArrayParameterSet
de.jstacs.parameters.
InstanceParameterSet
de.jstacs.data.
Alphabet.AlphabetParameterSet
de.jstacs.data.alphabets.
ContinuousAlphabet.ContinuousAlphabetParameterSet
de.jstacs.data.alphabets.
DiscreteAlphabet.DiscreteAlphabetParameterSet
de.jstacs.data.alphabets.
DNAAlphabet.DNAAlphabetParameterSet
de.jstacs.data.
AlphabetContainerParameterSet
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.
BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.
BTMutualInformation.BTMutualInformationParameterSet
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.
InhomogeneousMarkov.InhomogeneousMarkovParameterSet
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.
PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.
PMMMutualInformation.PMMMutualInformationParameterSet
de.jstacs.parameters.
SequenceScoringParameterSet
de.jstacs.scoringFunctions.directedGraphicalModels.
BayesianNetworkScoringFunctionParameterSet
de.jstacs.models.discrete.
DGMParameterSet
de.jstacs.models.discrete.homogeneous.parameters.
HomogeneousModelParameterSet
de.jstacs.models.discrete.homogeneous.parameters.
HomMMParameterSet
de.jstacs.models.discrete.inhomogeneous.parameters.
IDGMParameterSet
de.jstacs.models.discrete.inhomogeneous.parameters.
BayesianNetworkModelParameterSet
de.jstacs.models.discrete.inhomogeneous.parameters.
FSDAGMParameterSet
de.jstacs.models.mixture.gibbssampling.
FSDAGModelForGibbsSamplingParameterSet
de.jstacs.classifier.scoringFunctionBased.
ScoreClassifierParameterSet
de.jstacs.classifier.scoringFunctionBased.gendismix.
GenDisMixClassifierParameterSet
de.jstacs.parameters.
SimpleParameterSet
de.jstacs.io.
ParameterSetParser
de.jstacs.parameters.
ParameterSetTagger
de.jstacs.parameters.
ParameterSetTagger.KeyEntryComparator
<K,V> (implements java.util.
Comparator
<T>)
de.jstacs.parameters.
ParameterSetTagger.RankEntryComparator
<K,V> (implements java.util.
Comparator
<T>)
de.jstacs.scoringFunctions.directedGraphicalModels.
ParameterTree
(implements java.lang.
Cloneable
)
de.jstacs.models.mixture.motif.positionprior.
PositionPrior
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.models.mixture.motif.positionprior.
GaussianLikePositionPrior
de.jstacs.models.mixture.motif.positionprior.
UniformPositionPrior
de.jstacs.classifier.utils.
PValueComputation
de.jstacs.utils.random.
RandomNumberGenerator
(implements java.io.
Serializable
)
de.jstacs.parameters.validation.
ReferenceConstraint
(implements de.jstacs.parameters.validation.
Constraint
)
de.jstacs.parameters.validation.
SimpleReferenceConstraint
de.jstacs.utils.
REnvironment
de.jstacs.motifDiscovery.history.
RestrictedRepeatHistory
(implements de.jstacs.motifDiscovery.history.
History
)
de.jstacs.results.
Result
(implements de.jstacs.
Storable
)
de.jstacs.classifier.
AbstractScoreBasedClassifier.DoubleTableResult
de.jstacs.results.
ImageResult
de.jstacs.results.
ListResult
de.jstacs.results.
SampleResult
de.jstacs.results.
SimpleResult
(implements java.lang.
Comparable
<T>)
de.jstacs.results.
CategoricalResult
de.jstacs.results.
NumericalResult
de.jstacs.results.
StorableResult
de.jstacs.results.
ResultSet
(implements de.jstacs.
Storable
)
de.jstacs.results.
NumericalResultSet
de.jstacs.results.
MeanResultSet
de.jstacs.data.sequences.annotation.
SequenceAnnotation
de.jstacs.data.sequences.annotation.
CisRegulatoryModuleAnnotation
de.jstacs.data.sequences.annotation.
LocatedSequenceAnnotation
de.jstacs.data.sequences.annotation.
LocatedSequenceAnnotationWithLength
de.jstacs.data.sequences.annotation.
IntronAnnotation
de.jstacs.data.sequences.annotation.
StrandedLocatedSequenceAnnotationWithLength
de.jstacs.data.sequences.annotation.
MotifAnnotation
de.jstacs.data.sequences.annotation.
SinglePositionSequenceAnnotation
de.jstacs.utils.
RUtils
de.jstacs.data.
Sample
(implements java.lang.
Iterable
<T>)
de.jstacs.data.
DNASample
de.jstacs.data.
Sample.ElementEnumerator
(implements java.util.
Iterator
<E>, de.jstacs.data.
RecyclableSequenceEnumerator
)
de.jstacs.data.
Sample.WeightedSampleFactory
de.jstacs.data.
SampleKMerEnumerator
(implements de.jstacs.data.
RecyclableSequenceEnumerator
)
de.jstacs.classifier.
ScoreBasedPerformanceMeasureDefinitions
de.jstacs.classifier.
ScoreBasedPerformanceMeasureDefinitions.ThresholdMeasurePair
de.jstacs.data.
Sequence
(implements java.lang.
Comparable
<T>)
de.jstacs.data.sequences.
ArbitrarySequence
de.jstacs.data.sequences.
DiscreteSequence
de.jstacs.data.sequences.
ByteSequence
de.jstacs.data.sequences.
IntSequence
de.jstacs.data.sequences.
ShortSequence
de.jstacs.data.sequences.
SparseSequence
de.jstacs.data.sequences.
RecursiveSequence
de.jstacs.data.sequences.
PermutedSequence
de.jstacs.data.
Sequence.CompositeSequence
de.jstacs.data.
Sequence.SubSequence
de.jstacs.data.
SequenceEnumeration
(implements de.jstacs.data.
RecyclableSequenceEnumerator
)
de.jstacs.models.discrete.inhomogeneous.
SequenceIterator
(implements java.lang.
Cloneable
)
de.jstacs.motifDiscovery.
SignificantMotifOccurrencesFinder
de.jstacs.motifDiscovery.history.
SimpleHistory
(implements de.jstacs.motifDiscovery.history.
History
)
de.jstacs.data.sequences.annotation.
SimpleSequenceAnnotationParser
(implements de.jstacs.data.sequences.annotation.
SequenceAnnotationParser
)
de.jstacs.data.bioJava.
SimpleSequenceIterator
(implements org.biojava.bio.seq.
SequenceIterator
)
de.jstacs.parameters.validation.
SimpleStaticConstraint
(implements de.jstacs.parameters.validation.
Constraint
)
de.jstacs.algorithms.optimization.termination.
SmallDifferenceOfFunctionEvaluationsCondition
(implements de.jstacs.algorithms.optimization.termination.
TerminationCondition
)
de.jstacs.algorithms.optimization.termination.
SmallStepCondition
(implements de.jstacs.algorithms.optimization.termination.
TerminationCondition
)
de.jstacs.data.sequences.annotation.
SplitSequenceAnnotationParser
(implements de.jstacs.data.sequences.annotation.
SequenceAnnotationParser
)
de.jstacs.models.utils.
StationaryDistribution
de.jstacs.models.utils.
StatisticalTest
de.jstacs.parameters.validation.
StorableValidator
(implements de.jstacs.parameters.validation.
ParameterValidator
)
de.jstacs.models.discrete.inhomogeneous.
StructureLearner
de.jstacs.utils.
SubclassFinder
de.jstacs.io.
SymbolExtractor
(implements java.util.
Enumeration
<E>)
de.jstacs.algorithms.graphs.tensor.
Tensor
de.jstacs.algorithms.graphs.tensor.
AsymmetricTensor
de.jstacs.algorithms.graphs.tensor.
SubTensor
de.jstacs.algorithms.graphs.tensor.
SymmetricTensor
java.lang.
Throwable
(implements java.io.
Serializable
)
java.lang.
Exception
de.jstacs.classifier.
ClassDimensionException
de.jstacs.algorithms.optimization.
DimensionException
de.jstacs.data.alphabets.
DoubleSymbolException
de.jstacs.data.
EmptySampleException
de.jstacs.algorithms.optimization.
EvaluationException
de.jstacs.results.
MeanResultSet.AdditionImpossibleException
de.jstacs.results.
MeanResultSet.InconsistentResultNumberException
de.jstacs.
NonParsableException
de.jstacs.
NotTrainedException
de.jstacs.parameters.
ParameterException
de.jstacs.parameters.
CollectionParameter.InconsistentCollectionException
de.jstacs.io.
ParameterSetParser.NotInstantiableException
de.jstacs.io.
ParameterSetParser.WrongParameterTypeException
de.jstacs.parameters.
SimpleParameter.DatatypeNotValidException
de.jstacs.parameters.
SimpleParameter.IllegalValueException
de.jstacs.algorithms.optimization.
TerminationException
de.jstacs.
WrongAlphabetException
de.jstacs.data.
WrongLengthException
de.jstacs.data.sequences.
WrongSequenceTypeException
de.jstacs.utils.
Time
de.jstacs.utils.
RealTime
de.jstacs.utils.
UserTime
de.jstacs.algorithms.optimization.termination.
TimeCondition
(implements de.jstacs.algorithms.optimization.termination.
TerminationCondition
)
de.jstacs.utils.
ToolBox
de.jstacs.algorithms.graphs.
TopSort
de.jstacs.models.discrete.inhomogeneous.
TwoPointEvaluater
de.jstacs.algorithms.graphs.
UnionFind
de.jstacs.io.
XMLParser
Interface Hierarchy
de.jstacs.algorithms.
Alignment.Costs
java.lang.
Cloneable
de.jstacs.parameters.validation.
Constraint
(also extends de.jstacs.
Storable
)
de.jstacs.motifDiscovery.history.
History
de.jstacs.models.
Model
(also extends de.jstacs.
Storable
)
de.jstacs.motifDiscovery.
MotifDiscoverer
(also extends de.jstacs.
Storable
)
de.jstacs.motifDiscovery.
MutableMotifDiscoverer
de.jstacs.motifDiscovery.
MutableMotifDiscoverer
de.jstacs.scoringFunctions.
NormalizableScoringFunction
de.jstacs.scoringFunctions.
VariableLengthScoringFunction
de.jstacs.parameters.validation.
ParameterValidator
(also extends de.jstacs.
Storable
)
de.jstacs.scoringFunctions.
ScoringFunction
(also extends de.jstacs.
Storable
)
de.jstacs.scoringFunctions.
NormalizableScoringFunction
de.jstacs.scoringFunctions.
VariableLengthScoringFunction
de.jstacs.scoringFunctions.
VariableLengthScoringFunction
de.jstacs.scoringFunctions.
VariableLengthScoringFunction
java.util.
Enumeration
<E>
de.jstacs.data.
RecyclableSequenceEnumerator
de.jstacs.algorithms.optimization.
Function
de.jstacs.models.mixture.gibbssampling.
GibbsSamplingComponent
de.jstacs.
InstantiableFromParameterSet
de.jstacs.motifDiscovery.
Mutable
de.jstacs.utils.
ProgressUpdater
de.jstacs.parameters.
Rangeable
de.jstacs.parameters.
RangeIterator
de.jstacs.data.sequences.annotation.
SequenceAnnotationParser
de.jstacs.algorithms.optimization.
StartDistanceForecaster
de.jstacs.
Storable
de.jstacs.parameters.validation.
Constraint
(also extends java.lang.
Cloneable
)
de.jstacs.models.
Model
(also extends java.lang.
Cloneable
)
de.jstacs.motifDiscovery.
MotifDiscoverer
(also extends java.lang.
Cloneable
)
de.jstacs.motifDiscovery.
MutableMotifDiscoverer
de.jstacs.motifDiscovery.
MutableMotifDiscoverer
de.jstacs.scoringFunctions.
NormalizableScoringFunction
de.jstacs.scoringFunctions.
VariableLengthScoringFunction
de.jstacs.parameters.validation.
ParameterValidator
(also extends java.lang.
Cloneable
)
de.jstacs.scoringFunctions.
ScoringFunction
(also extends java.lang.
Cloneable
)
de.jstacs.scoringFunctions.
NormalizableScoringFunction
de.jstacs.scoringFunctions.
VariableLengthScoringFunction
de.jstacs.scoringFunctions.
VariableLengthScoringFunction
de.jstacs.scoringFunctions.
VariableLengthScoringFunction
de.jstacs.algorithms.optimization.termination.
TerminationCondition
Enum Hierarchy
java.lang.
Object
java.lang.
Enum
<E> (implements java.lang.
Comparable
<T>, java.io.
Serializable
)
de.jstacs.
DataType
de.jstacs.algorithms.
Alignment.Costs.Direction
de.jstacs.classifier.
MeasureParameters.Measure
de.jstacs.classifier.scoringFunctionBased.
OptimizableFunction.KindOfParameter
de.jstacs.classifier.scoringFunctionBased.gendismix.
LearningPrinciple
de.jstacs.data.
Sample.PartitionMethod
de.jstacs.data.
Sample.WeightedSampleFactory.SortOperation
de.jstacs.data.
AlphabetContainer.AlphabetContainerType
de.jstacs.data.sequences.annotation.
StrandedLocatedSequenceAnnotationWithLength.Strand
de.jstacs.data.sequences.annotation.
SinglePositionSequenceAnnotation.Type
de.jstacs.models.discrete.inhomogeneous.
StructureLearner.LearningType
de.jstacs.models.discrete.inhomogeneous.
StructureLearner.ModelType
de.jstacs.models.mixture.
AbstractMixtureModel.Parameterization
de.jstacs.models.mixture.
AbstractMixtureModel.Algorithm
de.jstacs.motifDiscovery.
SignificantMotifOccurrencesFinder.RandomSeqType
de.jstacs.motifDiscovery.
MutableMotifDiscovererToolbox.InitMethodForScoringFunction
de.jstacs.motifDiscovery.
MotifDiscoverer.KindOfProfile
de.jstacs.parameters.
RangeParameter.Scale
de.jstacs.parameters.
RangeParameter.RangeType
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.
BTMutualInformation.DataSource
de.jstacs.scoringFunctions.mix.
StrandScoringFunction.InitMethod
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